Scielo RSS <![CDATA[African Journal of Laboratory Medicine]]> vol. 8 num. 1 lang. en <![CDATA[SciELO Logo]]> <![CDATA[<b>Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa</b>]]> BACKGROUND: In sub-Saharan Africa, molecular epidemiological investigation of outbreaks caused by antimicrobial-resistant enteric bacterial pathogens have mostly been described for Salmonella species, Vibrio cholerae, Shigella species and Escherichia coli. For these organisms, I reviewed all publications describing the use of molecular subtyping methodologies to investigate outbreaks caused by multidrug-resistant (MDR) enteric bacterial infections. OBJECTIVES: To describe the use of molecular subtyping methodologies to investigate outbreaks caused by MDR enteric bacterial pathogens in sub-Saharan Africa and to describe the current status of molecular subtyping capabilities in the region. METHODS: A PubMed database literature search (English language only) was performed using the search strings: 'Africa outbreak MDR', 'Africa outbreak multi', 'Africa outbreak multidrug', 'Africa outbreak multi drug', 'Africa outbreak resistance', 'Africa outbreak resistant', 'Africa outbreak drug', 'Africa outbreak antibiotic', 'Africa outbreak antimicrobial'. These search strings were used in combination with genus and species names of the organisms listed above. All results were included in the review. RESULTS: The year 1991 saw one of the first reports describing the use of molecular subtyping methodologies in sub-Saharan Africa; this included the use of plasmid profiling to characterise Salmonella Enteritidis. To date, several methodologies have been used; pulsed-field gel electrophoresis analysis and multilocus sequence typing have been the most commonly used methodologies. Investigations have particularly highlighted the emergence and spread of MDR clones; these include Salmonella Typhi H58 and Salmonella Typhimurium ST313 clones. In recent times, whole-genome sequencing (WGS) analysis approaches have increasingly been used. CONCLUSION: Traditional molecular subtyping methodologies are still commonly used and still have their place in investigations; however, WGS approaches have increasingly been used and are slowly gaining a stronghold. African laboratories need to start adapting their molecular surveillance methodologies to include WGS, as it is foreseen that WGS analysis will eventually replace all traditional methodologies. <![CDATA[<b>Whole genome sequencing for drug resistance determination in <i>Mycobacterium tuberculosis</i></b>]]> South Africa remains challenged with a high tuberculosis burden accompanied by an increase in drug resistant cases. We assessed the use of the Illumina MiSeq, a next-generation sequencing platform for whole genome sequencing, followed by bioinformatic analysis using a commercial software package to determine resistance to selected drugs used for Mycobacterium tuberculosis treatment in our setting. Whole genome sequencing shows potential as a diagnostic platform for the detection of drug resistance in Mycobacterium tuberculosis with the provision of information for several drugs simultaneously. <![CDATA[<b>Implementation and evaluation of the Presto combined qualitative real-time assay for <i>Chlamydia trachomatis</i> and <i>Neisseria gonorrhoeae</i> in Rwanda</b>]]> BACKGROUND: The Presto combined qualitative real-time assay for Chlamydia trachomatis and Neisseria gonorrhoeae (Presto CT/NG PCR assay) is appealing for developing countries, because it can be used with multiple DNA extraction methods and polymerase chain reaction (PCR) platforms. OBJECTIVES: The objective of the study was to implement and evaluate the Presto CT/NG PCR assay at the National Reference Laboratory (NRL) in Kigali, Rwanda, where no real-time PCR assays for the detection of C. trachomatis or N. gonorrhoeae were available. METHODS: The Presto CT/NG PCR assay was first evaluated at the Institute of Tropical Medicine (ITM) in Antwerp, Belgium. Next, NRL laboratory technicians were trained to use the assay on their ABI PRISM 7500 real-time PCR instrument and their competencies were assessed prior to trial initiation. During the trial, endocervical swabs were tested at the NRL, with bi-monthly external quality control testing monitored by the ITM. The final NRL results were evaluated against extended gold standard testing at the ITM, consisting of the Abbott m2000 RealTime System with confirmation of positive results by an in-house real-time PCR assay for C. trachomatis or N. gonorrhoeae. RESULTS: Of the 192 samples analysed using the Presto assay at the NRL, 16 samples tested positive for C. trachomatis and 17 tested positive for N. gonorrhoeae; four of these were infected with both. The sensitivity and specificity of the Presto assay were 93.3% (95% confidence interval [CI]: 68.1% - 99.8%) and 99.4% (95% CI: 96.8% - 100%) for C. trachomatis and 100% (95% CI: 76.8% - 100%) and 98.8% (95% CI: 95.8% - 99.9%) for N. gonorrhoeae. CONCLUSION: C. trachomatis and N. gonorrhoeae testing with the Presto assay was feasible in Kigali, Rwanda, and good performance was achieved. <![CDATA[<b>Development and validation of a high performance liquid chromatography method to determine nevirapine in plasma in a resource-limited setting</b>]]> BACKGROUND: There are several instances where nevirapine pharmacokinetic monitoring may be useful, such as in special populations or pharmacokinetic drug interaction studies that require the ascertainment of nevirapine pharmacokinetics in the sub-Saharan region. OBJECTIVES: The main aim of this study was to produce a validated, sustainable and relevant nevirapine assay method that meets bio-analytical regulatory requirements. METHODS: The developed method utilised a Waters 2795 Alliance high performance liquid chromatography system with a 2996 photo diode array detector, an Atlantis dC18 5 micron, 3.9 mm × 150 mm analytical column and a gradient flow rate of 1 mL/min. Ultraviolet detection data were collected from 210 nm to 400 nm, extracted at 260 nm, and processed for nevirapine and internal standard peak height responses. RESULTS: The method proved to be linear (R2 0.995), precise (+1.92% - +9.69%) and accurate (-9.70% - 12.0%). Recovery for the analyte and internal standard was between 98.8% and 114%. The method showed good specificity as no interferences were caused by common African traditional medicines, anti-tuberculosis medications or other concomitant antiretrovirals nor endogenous components CONCLUSION: The method is reproducible, relevant to our setting and uses considerably low plasma volumes with preservation of some consumables, a desirable key factor in a resource-limited setting. <![CDATA[<b>Coexistence of Kaposi sarcoma and Molluscum contagiosum on the same site in a HIV-AIDS patient: A very rare occurrence</b>]]> INTRODUCTION: There have been numerous reported opportunistic infections among HIV/AIDS patients. However, coexistence of Kaposi sarcoma and Molluscum contagiosum on the same site is a rare finding. CASE PRESENTATION: A 37-year-old man poorly adherent to antiretroviral therapy presented with Molluscum contagiosum and Kaposi sarcoma occurring simultaneously on numerous skin lesions around mid-2017 at Usmanu Danfodiyo University Teaching Hospital, Sokoto State, Nigeria. MANAGEMENT AND OUTCOME: The patient was counselled and re-initiated on a second-line highly active antiretroviral therapy regimen. The patient's lesions resolved three months later. DISCUSSION: The case is presented to improve the index of suspicion among clinicians and pathologists on such rare occurrences. <![CDATA[<b>Utilisation of fine needle aspiration cytology and biopsy in Sokoto, Nigeria: A five-year review</b>]]> The histopathology department of Usmanu Danfodiyo University Teaching Hospital in Sokoto, Nigeria, conducted a total of 1435 fine needle aspiration biopsies from 1 January 2011 to 31 December 2015, constituting 30% of cytology specimens received. The most common site for the procedure was the breast (655 cases, 45.6%), and 893 cases (63.3%) were neoplastic lesions. Even in resource-poor settings, this underutilised procedure is useful for patient management.